/*
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 *    NumericTransform.java
 *    Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.filters.unsupervised.attribute;

import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.Enumeration;
import java.util.Vector;

import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.DenseInstance;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Range;
import weka.core.SparseInstance;
import weka.core.Utils;
import weka.core.WeightedAttributesHandler;
import weka.core.WeightedInstancesHandler;
import weka.filters.Filter;
import weka.filters.StreamableFilter;
import weka.filters.UnsupervisedFilter;

/**
 * <!-- globalinfo-start --> Transforms numeric attributes using a given
 * transformation method.
 * <p/>
 * <!-- globalinfo-end -->
 * 
 * <!-- options-start --> Valid options are:
 * <p/>
 * 
 * <pre>
 * -R &lt;index1,index2-index4,...&gt;
 *  Specify list of columns to transform. First and last are
 *  valid indexes (default none). Non-numeric columns are 
 *  skipped.
 * </pre>
 * 
 * <pre>
 * -V
 *  Invert matching sense.
 * </pre>
 * 
 * <pre>
 * -C &lt;string&gt;
 *  Sets the class containing transformation method.
 *  (default java.lang.Math)
 * </pre>
 * 
 * <pre>
 * -M &lt;string&gt;
 *  Sets the method. (default abs)
 * </pre>
 * 
 * <!-- options-end -->
 * 
 * @author Eibe Frank (eibe@cs.waikato.ac.nz)
 * @version $Revision$
 */
public class NumericTransform extends Filter implements UnsupervisedFilter, StreamableFilter, OptionHandler, WeightedInstancesHandler, WeightedAttributesHandler {

    /** for serialization */
    static final long serialVersionUID = -8561413333351366934L;

    /** Stores which columns to transform. */
    private final Range m_Cols = new Range();

    /** Class containing transformation method. */
    private String m_Class;

    /** Transformation method. */
    private String m_Method;

    /**
     * Returns a string describing this filter
     * 
     * @return a description of the filter suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String globalInfo() {

        return "Transforms numeric attributes using a given transformation method.";
    }

    /**
     * Default constructor -- sets the default transform method to
     * java.lang.Math.abs().
     */
    public NumericTransform() {

        m_Class = "java.lang.Math";
        m_Method = "abs";
    }

    /**
     * Returns the Capabilities of this filter.
     * 
     * @return the capabilities of this object
     * @see Capabilities
     */
    @Override
    public Capabilities getCapabilities() {
        Capabilities result = super.getCapabilities();
        result.disableAll();

        // attributes
        result.enableAllAttributes();
        result.enable(Capability.MISSING_VALUES);

        // class
        result.enableAllClasses();
        result.enable(Capability.MISSING_CLASS_VALUES);
        result.enable(Capability.NO_CLASS);

        return result;
    }

    /**
     * Sets the format of the input instances.
     * 
     * @param instanceInfo an Instances object containing the input instance
     *                     structure (any instances contained in the object are
     *                     ignored - only the structure is required).
     * @return true if the outputFormat may be collected immediately
     * @throws Exception if the input format can't be set successfully
     */
    @Override
    public boolean setInputFormat(Instances instanceInfo) throws Exception {

        if (m_Class == null) {
            throw new IllegalStateException("No class has been set.");
        }
        if (m_Method == null) {
            throw new IllegalStateException("No method has been set.");
        }
        super.setInputFormat(instanceInfo);
        m_Cols.setUpper(instanceInfo.numAttributes() - 1);
        setOutputFormat(instanceInfo);
        return true;
    }

    /**
     * Input an instance for filtering. The instance is processed and made available
     * for output immediately.
     * 
     * @param instance the input instance
     * @return true if the filtered instance may now be collected with output().
     * @throws IllegalStateException     if no input format has been set.
     * @throws InvocationTargetException if there is a problem applying the
     *                                   configured transform method.
     */
    @Override
    public boolean input(Instance instance) throws Exception {

        if (getInputFormat() == null) {
            throw new IllegalStateException("No input instance format defined");
        }
        if (m_NewBatch) {
            resetQueue();
            m_NewBatch = false;
        }

        Method m = (Class.forName(m_Class)).getMethod(m_Method, new Class[] { Double.TYPE });

        double[] vals = new double[instance.numAttributes()];
        Double[] params = new Double[1];
        Double newVal;
        for (int i = 0; i < instance.numAttributes(); i++) {
            if (instance.isMissing(i)) {
                vals[i] = Utils.missingValue();
            } else {
                if (m_Cols.isInRange(i) && instance.attribute(i).isNumeric()) {
                    params[0] = new Double(instance.value(i));
                    newVal = (Double) m.invoke(null, (Object[]) params);
                    if (newVal.isNaN() || newVal.isInfinite()) {
                        vals[i] = Utils.missingValue();
                    } else {
                        vals[i] = newVal.doubleValue();
                    }
                } else {
                    vals[i] = instance.value(i);
                }
            }
        }
        Instance inst = null;
        if (instance instanceof SparseInstance) {
            inst = new SparseInstance(instance.weight(), vals);
        } else {
            inst = new DenseInstance(instance.weight(), vals);
        }
        inst.setDataset(instance.dataset());
        push(inst, false); // No need to copy
        return true;
    }

    /**
     * Returns an enumeration describing the available options.
     * 
     * @return an enumeration of all the available options.
     */
    @Override
    public Enumeration<Option> listOptions() {

        Vector<Option> newVector = new Vector<Option>(4);

        newVector.addElement(new Option("\tSpecify list of columns to transform. First and last are\n" + "\tvalid indexes (default none). Non-numeric columns are \n" + "\tskipped.", "R", 1, "-R <index1,index2-index4,...>"));

        newVector.addElement(new Option("\tInvert matching sense.", "V", 0, "-V"));

        newVector.addElement(new Option("\tSets the class containing transformation method.\n" + "\t(default java.lang.Math)", "C", 1, "-C <string>"));

        newVector.addElement(new Option("\tSets the method. (default abs)", "M", 1, "-M <string>"));

        return newVector.elements();
    }

    /**
     * Parses a given list of options.
     * <p/>
     * 
     * <!-- options-start --> Valid options are:
     * <p/>
     * 
     * <pre>
     * -R &lt;index1,index2-index4,...&gt;
     *  Specify list of columns to transform. First and last are
     *  valid indexes (default none). Non-numeric columns are 
     *  skipped.
     * </pre>
     * 
     * <pre>
     * -V
     *  Invert matching sense.
     * </pre>
     * 
     * <pre>
     * -C &lt;string&gt;
     *  Sets the class containing transformation method.
     *  (default java.lang.Math)
     * </pre>
     * 
     * <pre>
     * -M &lt;string&gt;
     *  Sets the method. (default abs)
     * </pre>
     * 
     * <!-- options-end -->
     * 
     * @param options the list of options as an array of strings
     * @throws Exception if an option is not supported
     */
    @Override
    public void setOptions(String[] options) throws Exception {

        setAttributeIndices(Utils.getOption('R', options));
        setInvertSelection(Utils.getFlag('V', options));
        String classString = Utils.getOption('C', options);
        if (classString.length() != 0) {
            setClassName(classString);
        }
        String methodString = Utils.getOption('M', options);
        if (methodString.length() != 0) {
            setMethodName(methodString);
        }

        if (getInputFormat() != null) {
            setInputFormat(getInputFormat());
        }

        Utils.checkForRemainingOptions(options);
    }

    /**
     * Gets the current settings of the filter.
     * 
     * @return an array of strings suitable for passing to setOptions
     */
    @Override
    public String[] getOptions() {

        Vector<String> options = new Vector<String>();

        if (getInvertSelection()) {
            options.add("-V");
        }
        if (!getAttributeIndices().equals("")) {
            options.add("-R");
            options.add(getAttributeIndices());
        }
        if (m_Class != null) {
            options.add("-C");
            options.add(getClassName());
        }
        if (m_Method != null) {
            options.add("-M");
            options.add(getMethodName());
        }

        return options.toArray(new String[0]);
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String classNameTipText() {
        return "Name of the class containing the method used for the transformation.";
    }

    /**
     * Get the class containing the transformation method.
     * 
     * @return string describing the class
     */
    public String getClassName() {

        return m_Class;
    }

    /**
     * Sets the class containing the transformation method.
     * 
     * @param name the name of the class
     * @throws ClassNotFoundException if class can't be found
     */
    public void setClassName(String name) throws ClassNotFoundException {

        m_Class = name;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String methodNameTipText() {
        return "Name of the method used for the transformation.";
    }

    /**
     * Get the transformation method.
     * 
     * @return string describing the transformation method.
     */
    public String getMethodName() {

        return m_Method;
    }

    /**
     * Set the transformation method.
     * 
     * @param name the name of the method
     * @throws NoSuchMethodException if method can't be found in class
     */
    public void setMethodName(String name) throws NoSuchMethodException {

        m_Method = name;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String invertSelectionTipText() {
        return "Whether to process the inverse of the given attribute ranges.";
    }

    /**
     * Get whether the supplied columns are to be transformed or not
     * 
     * @return true if the supplied columns will be kept
     */
    public boolean getInvertSelection() {

        return m_Cols.getInvert();
    }

    /**
     * Set whether selected columns should be transformed or not.
     * 
     * @param invert the new invert setting
     */
    public void setInvertSelection(boolean invert) {

        m_Cols.setInvert(invert);
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String attributeIndicesTipText() {
        return "Specify range of attributes to act on." + " This is a comma separated list of attribute indices, with" + " \"first\" and \"last\" valid values. Specify an inclusive" + " range with \"-\". E.g: \"first-3,5,6-10,last\".";
    }

    /**
     * Get the current range selection
     * 
     * @return a string containing a comma separated list of ranges
     */
    public String getAttributeIndices() {

        return m_Cols.getRanges();
    }

    /**
     * Set which attributes are to be transformed (or kept if invert is true).
     * 
     * @param rangeList a string representing the list of attributes. Since the
     *                  string will typically come from a user, attributes are
     *                  indexed from 1. <br>
     *                  eg: first-3,5,6-last
     */

    public void setAttributeIndices(String rangeList) {

        m_Cols.setRanges(rangeList);
    }

    /**
     * Set which attributes are to be transformed (or kept if invert is true)
     * 
     * @param attributes an array containing indexes of attributes to select. Since
     *                   the array will typically come from a program, attributes
     *                   are indexed from 0.
     */
    public void setAttributeIndicesArray(int[] attributes) {

        setAttributeIndices(Range.indicesToRangeList(attributes));
    }

    /**
     * Main method for testing this class.
     * 
     * @param argv should contain arguments to the filter: use -h for help
     */
    public static void main(String[] argv) {
        runFilter(new NumericTransform(), argv);
    }
}
